aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/index.h
blob: 31ee43396cdeebbeb3a848a5e14d58c06387e07c (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
/*
 * index.h
 *
 * Perform indexing (somehow)
 *
 * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 * Copyright © 2012 Richard Kirian
 * Copyright © 2012 Lorenzo Galli
 *
 * Authors:
 *   2010-2013 Thomas White <taw@physics.org>
 *   2010      Richard Kirian
 *   2012      Lorenzo Galli
 *
 * This file is part of CrystFEL.
 *
 * CrystFEL is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * CrystFEL is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#ifndef INDEX_H
#define INDEX_H

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif


#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS         \
                                     | INDEXING_CHECK_CELL_COMBINATIONS)

#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS       \
                                     | INDEXING_CHECK_CELL_COMBINATIONS        \
                                     | INDEXING_USE_LATTICE_TYPE)

#define INDEXING_DEFAULTS_REAX (INDEXING_REAX | INDEXING_USE_LATTICE_TYPE      \
                                     | INDEXING_USE_CELL_PARAMETERS            \
                                     | INDEXING_CHECK_PEAKS)

#define INDEXING_DEFAULTS_GRAINSPOTTER (INDEXING_GRAINSPOTTER                  \
                                     | INDEXING_USE_LATTICE_TYPE               \
                                     | INDEXING_USE_CELL_PARAMETERS            \
                                     | INDEXING_CHECK_PEAKS)

#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE        \
                                     | INDEXING_USE_CELL_PARAMETERS            \
                                     | INDEXING_CHECK_PEAKS)

/**
 * IndexingMethod:
 * @INDEXING_NONE: No indexing to be performed
 * @INDEXING_DIRAX: Invoke DirAx
 * @INDEXING_MOSFLM: Invoke MOSFLM
 * @INDEXING_REAX: DPS algorithm using known cell parameters
 * @INDEXING_GRAINSPOTTER: Invoke GrainSpotter
 * @INDEXING_XDS: Invokve XDS
 * @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell
 *   axes for agreement with given cell.
 * @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given
 *   cell, and permute them if necessary.
 * @INDEXING_CHECK_PEAKS: Check that the peaks can be explained by the indexing
 *   result.
 * @INDEXING_USE_LATTICE_TYPE: Use lattice type and centering information to
 *   guide the indexing process.
 * @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
 *   indexingprocess.
 *
 * An enumeration of all the available indexing methods.
 **/
typedef enum {

	INDEXING_NONE   = 0,

	/* The core indexing methods themselves */
	INDEXING_DIRAX  = 1,
	INDEXING_MOSFLM = 2,
	INDEXING_REAX   = 3,
	INDEXING_GRAINSPOTTER = 4,
        INDEXING_XDS = 5,

	/* Bits at the top of the IndexingMethod are flags which modify the
	 * behaviour of the indexer. */
	INDEXING_CHECK_CELL_COMBINATIONS = 256,
	INDEXING_CHECK_CELL_AXES         = 512,
	INDEXING_CHECK_PEAKS             = 1024,
	INDEXING_USE_LATTICE_TYPE        = 2048,
	INDEXING_USE_CELL_PARAMETERS     = 4096,

} IndexingMethod;

/* This defines the bits in "IndexingMethod" which are used to represent the
 * core of the indexing method */
#define INDEXING_METHOD_MASK (0xff)


/**
 * IndexingPrivate:
 *
 * This is an opaque data structure containing information needed by the
 * indexing method.
 **/
typedef void *IndexingPrivate;

extern IndexingMethod *build_indexer_list(const char *str);
extern char *indexer_str(IndexingMethod indm);

#include "beam-parameters.h"
#include "detector.h"
#include "cell.h"
#include "image.h"

extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
                                          const char *filename,
                                          struct detector *det,
                                          struct beam_params *beam, float *ltl);

extern void index_pattern(struct image *image,
                          IndexingMethod *indms, IndexingPrivate **iprivs);

extern void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs);

#endif	/* INDEX_H */